Multiple sequence alignment - TraesCS3A01G176700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G176700 chr3A 100.000 3697 0 0 822 4518 198034386 198038082 0.000000e+00 6828.0
1 TraesCS3A01G176700 chr3A 100.000 364 0 0 1 364 198033565 198033928 0.000000e+00 673.0
2 TraesCS3A01G176700 chr3A 100.000 108 0 0 4819 4926 198038383 198038490 3.010000e-47 200.0
3 TraesCS3A01G176700 chr2A 95.372 3133 117 5 823 3929 235821718 235824848 0.000000e+00 4957.0
4 TraesCS3A01G176700 chr2A 94.350 1292 48 9 3242 4510 235877995 235879284 0.000000e+00 1958.0
5 TraesCS3A01G176700 chr2A 97.161 1092 25 4 1407 2495 362052813 362053901 0.000000e+00 1840.0
6 TraesCS3A01G176700 chr2A 96.472 907 32 0 2522 3428 362053897 362054803 0.000000e+00 1498.0
7 TraesCS3A01G176700 chr2A 95.238 252 10 2 113 364 235821397 235821646 9.940000e-107 398.0
8 TraesCS3A01G176700 chr2A 94.444 108 5 1 4819 4926 235879428 235879534 1.100000e-36 165.0
9 TraesCS3A01G176700 chr2A 95.918 98 4 0 2372 2469 68155824 68155921 5.100000e-35 159.0
10 TraesCS3A01G176700 chr2A 92.661 109 7 1 2372 2480 660286871 660286764 6.600000e-34 156.0
11 TraesCS3A01G176700 chr2A 89.888 89 4 3 1329 1412 12363671 12363583 5.210000e-20 110.0
12 TraesCS3A01G176700 chr5A 95.196 2248 106 2 902 3147 90043183 90045430 0.000000e+00 3552.0
13 TraesCS3A01G176700 chr5A 93.634 1398 62 8 3142 4518 90090094 90091485 0.000000e+00 2063.0
14 TraesCS3A01G176700 chr5A 84.530 989 95 23 3467 4422 687471022 687471985 0.000000e+00 926.0
15 TraesCS3A01G176700 chr2D 96.925 2016 57 5 1415 3428 294974989 294977001 0.000000e+00 3374.0
16 TraesCS3A01G176700 chr2D 96.041 783 29 2 1368 2148 205891169 205890387 0.000000e+00 1273.0
17 TraesCS3A01G176700 chr2D 93.227 812 49 4 3429 4237 341648022 341648830 0.000000e+00 1190.0
18 TraesCS3A01G176700 chr2D 90.952 420 20 3 4117 4518 409429049 409429468 2.590000e-152 549.0
19 TraesCS3A01G176700 chr2D 85.199 527 38 20 822 1321 341647498 341648011 5.690000e-139 505.0
20 TraesCS3A01G176700 chr7B 93.021 1089 49 11 3429 4496 448501238 448500156 0.000000e+00 1565.0
21 TraesCS3A01G176700 chr7B 90.000 420 23 4 4117 4518 347102723 347102305 4.370000e-145 525.0
22 TraesCS3A01G176700 chr7B 91.202 341 22 5 3763 4102 374713512 374713179 1.620000e-124 457.0
23 TraesCS3A01G176700 chr7B 86.236 356 25 5 823 1178 448501783 448501452 1.010000e-96 364.0
24 TraesCS3A01G176700 chr7B 87.814 279 25 7 92 364 448502130 448501855 7.960000e-83 318.0
25 TraesCS3A01G176700 chr7B 94.937 158 8 0 3604 3761 374713965 374713808 1.060000e-61 248.0
26 TraesCS3A01G176700 chr7B 90.625 160 14 1 1171 1329 448501398 448501239 1.390000e-50 211.0
27 TraesCS3A01G176700 chr7B 95.283 106 5 0 4819 4924 399541293 399541398 8.480000e-38 169.0
28 TraesCS3A01G176700 chr7B 94.340 106 6 0 4819 4924 448499718 448499613 3.950000e-36 163.0
29 TraesCS3A01G176700 chr7B 90.698 86 3 2 1332 1412 232301804 232301889 5.210000e-20 110.0
30 TraesCS3A01G176700 chr7B 86.000 100 9 1 1330 1424 29315590 29315689 8.720000e-18 102.0
31 TraesCS3A01G176700 chr2B 95.501 778 20 6 1407 2175 354074821 354074050 0.000000e+00 1229.0
32 TraesCS3A01G176700 chr2B 95.497 755 31 2 2674 3428 354073610 354072859 0.000000e+00 1203.0
33 TraesCS3A01G176700 chr2B 97.285 221 5 1 2455 2675 354073912 354073693 1.670000e-99 374.0
34 TraesCS3A01G176700 chr2B 97.917 144 3 0 2224 2367 354074053 354073910 2.940000e-62 250.0
35 TraesCS3A01G176700 chr2B 95.283 106 5 0 4819 4924 342169019 342168914 8.480000e-38 169.0
36 TraesCS3A01G176700 chr6A 93.262 846 32 8 3695 4518 139066474 139067316 0.000000e+00 1223.0
37 TraesCS3A01G176700 chr6A 93.243 814 47 6 3429 4237 513611075 513611885 0.000000e+00 1192.0
38 TraesCS3A01G176700 chr6A 92.553 846 38 8 3695 4518 409751350 409750508 0.000000e+00 1190.0
39 TraesCS3A01G176700 chr6A 93.129 815 49 5 3429 4239 162237325 162236514 0.000000e+00 1188.0
40 TraesCS3A01G176700 chr6A 87.151 537 39 15 822 1329 513610539 513611074 2.560000e-162 582.0
41 TraesCS3A01G176700 chr6A 87.127 536 40 14 822 1329 162237860 162237326 9.190000e-162 580.0
42 TraesCS3A01G176700 chr6A 89.437 142 15 0 3429 3570 78045396 78045537 3.920000e-41 180.0
43 TraesCS3A01G176700 chr6A 95.283 106 5 0 4819 4924 409750367 409750262 8.480000e-38 169.0
44 TraesCS3A01G176700 chr6A 95.283 106 5 0 4819 4924 421537062 421537167 8.480000e-38 169.0
45 TraesCS3A01G176700 chr6A 94.340 106 6 0 4819 4924 139067460 139067565 3.950000e-36 163.0
46 TraesCS3A01G176700 chr6A 83.333 72 8 4 93 162 118677979 118677910 4.120000e-06 63.9
47 TraesCS3A01G176700 chr7A 93.481 813 47 4 3429 4237 341321484 341322294 0.000000e+00 1203.0
48 TraesCS3A01G176700 chr7A 85.066 529 49 17 822 1321 341320945 341321472 3.400000e-141 512.0
49 TraesCS3A01G176700 chr7A 95.570 158 7 0 3604 3761 427811219 427811062 2.280000e-63 254.0
50 TraesCS3A01G176700 chr7A 95.283 106 5 0 4819 4924 285048597 285048702 8.480000e-38 169.0
51 TraesCS3A01G176700 chr7A 77.236 246 35 16 93 323 623650526 623650765 1.860000e-24 124.0
52 TraesCS3A01G176700 chr1A 92.080 846 41 9 3695 4518 90940001 90939160 0.000000e+00 1168.0
53 TraesCS3A01G176700 chr1A 85.868 651 69 11 3776 4423 130929287 130929917 0.000000e+00 671.0
54 TraesCS3A01G176700 chr1A 89.958 239 19 3 3467 3702 130929001 130929237 2.230000e-78 303.0
55 TraesCS3A01G176700 chr1A 88.732 142 16 0 3429 3570 130933461 130933602 1.820000e-39 174.0
56 TraesCS3A01G176700 chr1A 81.675 191 27 4 1053 1236 464426264 464426453 8.540000e-33 152.0
57 TraesCS3A01G176700 chr1A 97.561 41 1 0 3690 3730 130929251 130929291 2.460000e-08 71.3
58 TraesCS3A01G176700 chr3D 91.169 419 19 3 4118 4518 332866408 332866826 2.000000e-153 553.0
59 TraesCS3A01G176700 chr3D 95.283 106 5 0 4819 4924 332866966 332867071 8.480000e-38 169.0
60 TraesCS3A01G176700 chr3D 95.960 99 4 0 2371 2469 71512811 71512909 1.420000e-35 161.0
61 TraesCS3A01G176700 chr7D 90.976 410 19 3 4119 4510 527214630 527215039 2.020000e-148 536.0
62 TraesCS3A01G176700 chr7D 91.000 400 18 3 4117 4498 527507107 527507506 1.570000e-144 523.0
63 TraesCS3A01G176700 chr7D 90.024 411 22 4 4119 4510 526992563 526992973 9.460000e-142 514.0
64 TraesCS3A01G176700 chr7D 90.476 336 23 6 3763 4097 379322177 379321850 7.570000e-118 435.0
65 TraesCS3A01G176700 chr7D 96.835 158 5 0 3604 3761 379322537 379322380 1.050000e-66 265.0
66 TraesCS3A01G176700 chr7D 93.396 106 6 1 4819 4924 527507949 527508053 6.600000e-34 156.0
67 TraesCS3A01G176700 chr7D 100.000 77 0 0 1 77 515100679 515100755 5.140000e-30 143.0
68 TraesCS3A01G176700 chr4D 84.328 536 41 24 822 1328 281391180 281390659 7.410000e-133 484.0
69 TraesCS3A01G176700 chr4D 90.580 276 20 6 4152 4425 304655256 304654985 1.300000e-95 361.0
70 TraesCS3A01G176700 chr4D 91.083 157 13 1 3429 3584 281390657 281390501 1.390000e-50 211.0
71 TraesCS3A01G176700 chr4D 98.701 77 1 0 1 77 214410741 214410665 2.390000e-28 137.0
72 TraesCS3A01G176700 chr4D 98.701 77 1 0 1 77 287009467 287009391 2.390000e-28 137.0
73 TraesCS3A01G176700 chr4D 98.701 77 1 0 1 77 297430900 297430976 2.390000e-28 137.0
74 TraesCS3A01G176700 chr4D 89.773 88 4 2 1331 1413 17133651 17133564 1.880000e-19 108.0
75 TraesCS3A01G176700 chr1D 86.859 312 34 6 4115 4423 61892647 61892954 4.720000e-90 342.0
76 TraesCS3A01G176700 chr1D 90.598 117 9 2 2362 2477 225936957 225936842 2.370000e-33 154.0
77 TraesCS3A01G176700 chr1D 90.909 77 6 1 3429 3504 185919928 185919852 8.720000e-18 102.0
78 TraesCS3A01G176700 chr4A 90.141 142 14 0 3429 3570 28769238 28769097 8.420000e-43 185.0
79 TraesCS3A01G176700 chr4A 89.888 89 4 2 1329 1412 599432663 599432751 5.210000e-20 110.0
80 TraesCS3A01G176700 chr4B 96.226 106 4 0 4819 4924 162840354 162840249 1.820000e-39 174.0
81 TraesCS3A01G176700 chr5D 95.000 100 5 0 2372 2471 521371581 521371680 1.840000e-34 158.0
82 TraesCS3A01G176700 chr6D 98.701 77 1 0 1 77 87654225 87654301 2.390000e-28 137.0
83 TraesCS3A01G176700 chr6D 98.701 77 1 0 1 77 101612747 101612671 2.390000e-28 137.0
84 TraesCS3A01G176700 chr6D 98.701 77 1 0 1 77 255323613 255323537 2.390000e-28 137.0
85 TraesCS3A01G176700 chr6D 98.701 77 1 0 1 77 354449401 354449477 2.390000e-28 137.0
86 TraesCS3A01G176700 chr6D 98.701 77 1 0 1 77 358756901 358756825 2.390000e-28 137.0
87 TraesCS3A01G176700 chr6B 88.172 93 6 3 1332 1419 634283500 634283592 6.740000e-19 106.0
88 TraesCS3A01G176700 chr6B 100.000 38 0 0 93 130 409345768 409345731 2.460000e-08 71.3
89 TraesCS3A01G176700 chr5B 89.831 59 5 1 1264 1321 173796072 173796130 1.900000e-09 75.0
90 TraesCS3A01G176700 chr5B 88.136 59 6 1 1264 1321 530879460 530879518 8.850000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G176700 chr3A 198033565 198038490 4925 False 2567.000 6828 100.00000 1 4926 3 chr3A.!!$F1 4925
1 TraesCS3A01G176700 chr2A 235821397 235824848 3451 False 2677.500 4957 95.30500 113 3929 2 chr2A.!!$F2 3816
2 TraesCS3A01G176700 chr2A 362052813 362054803 1990 False 1669.000 1840 96.81650 1407 3428 2 chr2A.!!$F4 2021
3 TraesCS3A01G176700 chr2A 235877995 235879534 1539 False 1061.500 1958 94.39700 3242 4926 2 chr2A.!!$F3 1684
4 TraesCS3A01G176700 chr5A 90043183 90045430 2247 False 3552.000 3552 95.19600 902 3147 1 chr5A.!!$F1 2245
5 TraesCS3A01G176700 chr5A 90090094 90091485 1391 False 2063.000 2063 93.63400 3142 4518 1 chr5A.!!$F2 1376
6 TraesCS3A01G176700 chr5A 687471022 687471985 963 False 926.000 926 84.53000 3467 4422 1 chr5A.!!$F3 955
7 TraesCS3A01G176700 chr2D 294974989 294977001 2012 False 3374.000 3374 96.92500 1415 3428 1 chr2D.!!$F1 2013
8 TraesCS3A01G176700 chr2D 205890387 205891169 782 True 1273.000 1273 96.04100 1368 2148 1 chr2D.!!$R1 780
9 TraesCS3A01G176700 chr2D 341647498 341648830 1332 False 847.500 1190 89.21300 822 4237 2 chr2D.!!$F3 3415
10 TraesCS3A01G176700 chr7B 448499613 448502130 2517 True 524.200 1565 90.40720 92 4924 5 chr7B.!!$R3 4832
11 TraesCS3A01G176700 chr7B 374713179 374713965 786 True 352.500 457 93.06950 3604 4102 2 chr7B.!!$R2 498
12 TraesCS3A01G176700 chr2B 354072859 354074821 1962 True 764.000 1229 96.55000 1407 3428 4 chr2B.!!$R2 2021
13 TraesCS3A01G176700 chr6A 513610539 513611885 1346 False 887.000 1192 90.19700 822 4237 2 chr6A.!!$F4 3415
14 TraesCS3A01G176700 chr6A 162236514 162237860 1346 True 884.000 1188 90.12800 822 4239 2 chr6A.!!$R2 3417
15 TraesCS3A01G176700 chr6A 139066474 139067565 1091 False 693.000 1223 93.80100 3695 4924 2 chr6A.!!$F3 1229
16 TraesCS3A01G176700 chr6A 409750262 409751350 1088 True 679.500 1190 93.91800 3695 4924 2 chr6A.!!$R3 1229
17 TraesCS3A01G176700 chr7A 341320945 341322294 1349 False 857.500 1203 89.27350 822 4237 2 chr7A.!!$F3 3415
18 TraesCS3A01G176700 chr1A 90939160 90940001 841 True 1168.000 1168 92.08000 3695 4518 1 chr1A.!!$R1 823
19 TraesCS3A01G176700 chr1A 130929001 130933602 4601 False 304.825 671 90.52975 3429 4423 4 chr1A.!!$F2 994
20 TraesCS3A01G176700 chr3D 332866408 332867071 663 False 361.000 553 93.22600 4118 4924 2 chr3D.!!$F2 806
21 TraesCS3A01G176700 chr7D 379321850 379322537 687 True 350.000 435 93.65550 3604 4097 2 chr7D.!!$R1 493
22 TraesCS3A01G176700 chr7D 527507107 527508053 946 False 339.500 523 92.19800 4117 4924 2 chr7D.!!$F4 807
23 TraesCS3A01G176700 chr4D 281390501 281391180 679 True 347.500 484 87.70550 822 3584 2 chr4D.!!$R5 2762

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
56 57 0.957362 TGCGATGCCAATTTGTGTCA 59.043 45.0 0.0 0.0 0.00 3.58 F
1226 1308 0.613260 ATGCTACTGCCACCTTCGAA 59.387 50.0 0.0 0.0 38.71 3.71 F
2993 3205 0.842030 ATCTTGGACTGGAGCACCCA 60.842 55.0 0.0 0.0 44.25 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2047 2145 0.252103 AAGCCCCGAGTGAGACCTTA 60.252 55.0 0.00 0.0 0.0 2.69 R
3156 3368 0.468226 TCCCGCTTCTCACAACTGTT 59.532 50.0 0.00 0.0 0.0 3.16 R
4426 4972 0.657840 ACTTGCGTGCACTTGTTCTC 59.342 50.0 16.19 0.0 0.0 2.87 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 7.960793 GGTAGATACCGTATCATGTTAAATGC 58.039 38.462 18.67 1.70 37.65 3.56
40 41 6.706055 AGATACCGTATCATGTTAAATGCG 57.294 37.500 18.67 0.00 37.65 4.73
41 42 6.452242 AGATACCGTATCATGTTAAATGCGA 58.548 36.000 18.67 0.00 37.65 5.10
42 43 7.097192 AGATACCGTATCATGTTAAATGCGAT 58.903 34.615 18.67 0.00 37.65 4.58
43 44 5.342806 ACCGTATCATGTTAAATGCGATG 57.657 39.130 4.54 0.00 33.56 3.84
44 45 4.151070 CCGTATCATGTTAAATGCGATGC 58.849 43.478 4.54 0.00 33.56 3.91
45 46 4.151070 CGTATCATGTTAAATGCGATGCC 58.849 43.478 0.00 0.00 33.56 4.40
46 47 4.319405 CGTATCATGTTAAATGCGATGCCA 60.319 41.667 0.00 0.00 33.56 4.92
47 48 4.652421 ATCATGTTAAATGCGATGCCAA 57.348 36.364 0.00 0.00 0.00 4.52
48 49 4.652421 TCATGTTAAATGCGATGCCAAT 57.348 36.364 0.00 0.00 0.00 3.16
49 50 5.008619 TCATGTTAAATGCGATGCCAATT 57.991 34.783 0.00 0.00 0.00 2.32
50 51 5.417811 TCATGTTAAATGCGATGCCAATTT 58.582 33.333 0.00 0.00 0.00 1.82
51 52 5.291371 TCATGTTAAATGCGATGCCAATTTG 59.709 36.000 0.00 0.00 0.00 2.32
52 53 4.564041 TGTTAAATGCGATGCCAATTTGT 58.436 34.783 0.00 0.00 0.00 2.83
53 54 4.388165 TGTTAAATGCGATGCCAATTTGTG 59.612 37.500 0.00 0.00 0.00 3.33
54 55 2.747396 AATGCGATGCCAATTTGTGT 57.253 40.000 0.00 0.00 0.00 3.72
55 56 2.282701 ATGCGATGCCAATTTGTGTC 57.717 45.000 0.00 0.00 0.00 3.67
56 57 0.957362 TGCGATGCCAATTTGTGTCA 59.043 45.000 0.00 0.00 0.00 3.58
57 58 1.545136 TGCGATGCCAATTTGTGTCAT 59.455 42.857 0.00 0.00 0.00 3.06
58 59 1.921887 GCGATGCCAATTTGTGTCATG 59.078 47.619 0.00 0.00 0.00 3.07
59 60 1.921887 CGATGCCAATTTGTGTCATGC 59.078 47.619 0.00 0.00 0.00 4.06
60 61 2.671632 CGATGCCAATTTGTGTCATGCA 60.672 45.455 0.00 0.00 0.00 3.96
61 62 3.527533 GATGCCAATTTGTGTCATGCAT 58.472 40.909 7.87 7.87 40.37 3.96
62 63 2.689646 TGCCAATTTGTGTCATGCATG 58.310 42.857 21.07 21.07 0.00 4.06
63 64 2.004017 GCCAATTTGTGTCATGCATGG 58.996 47.619 25.97 9.04 0.00 3.66
64 65 2.004017 CCAATTTGTGTCATGCATGGC 58.996 47.619 24.40 24.40 0.00 4.40
65 66 2.613223 CCAATTTGTGTCATGCATGGCA 60.613 45.455 29.45 29.45 44.86 4.92
66 67 3.067833 CAATTTGTGTCATGCATGGCAA 58.932 40.909 34.01 25.74 44.94 4.52
67 68 3.620427 ATTTGTGTCATGCATGGCAAT 57.380 38.095 34.01 21.63 44.94 3.56
68 69 4.739587 ATTTGTGTCATGCATGGCAATA 57.260 36.364 34.01 22.99 44.94 1.90
69 70 4.532314 TTTGTGTCATGCATGGCAATAA 57.468 36.364 34.01 26.82 44.94 1.40
70 71 4.532314 TTGTGTCATGCATGGCAATAAA 57.468 36.364 34.01 24.20 44.94 1.40
71 72 4.739587 TGTGTCATGCATGGCAATAAAT 57.260 36.364 34.01 0.00 44.94 1.40
72 73 5.848833 TGTGTCATGCATGGCAATAAATA 57.151 34.783 34.01 14.13 44.94 1.40
73 74 6.408107 TGTGTCATGCATGGCAATAAATAT 57.592 33.333 34.01 0.00 44.94 1.28
74 75 6.217294 TGTGTCATGCATGGCAATAAATATG 58.783 36.000 34.01 1.77 44.94 1.78
75 76 6.040616 TGTGTCATGCATGGCAATAAATATGA 59.959 34.615 34.01 6.03 44.94 2.15
76 77 7.094631 GTGTCATGCATGGCAATAAATATGAT 58.905 34.615 34.01 0.00 44.94 2.45
77 78 7.062956 GTGTCATGCATGGCAATAAATATGATG 59.937 37.037 34.01 0.12 44.94 3.07
78 79 6.035650 GTCATGCATGGCAATAAATATGATGC 59.964 38.462 26.04 0.00 43.62 3.91
79 80 5.470047 TGCATGGCAATAAATATGATGCA 57.530 34.783 0.00 0.00 41.69 3.96
80 81 6.043854 TGCATGGCAATAAATATGATGCAT 57.956 33.333 0.00 0.00 39.70 3.96
81 82 5.872070 TGCATGGCAATAAATATGATGCATG 59.128 36.000 2.46 0.00 39.70 4.06
82 83 5.220586 GCATGGCAATAAATATGATGCATGC 60.221 40.000 11.82 11.82 41.36 4.06
86 87 6.160664 GCAATAAATATGATGCATGCCAAC 57.839 37.500 16.68 7.07 38.63 3.77
87 88 5.929992 GCAATAAATATGATGCATGCCAACT 59.070 36.000 16.68 0.00 38.63 3.16
88 89 7.092079 GCAATAAATATGATGCATGCCAACTA 58.908 34.615 16.68 2.38 38.63 2.24
89 90 7.274904 GCAATAAATATGATGCATGCCAACTAG 59.725 37.037 16.68 0.00 38.63 2.57
90 91 8.517056 CAATAAATATGATGCATGCCAACTAGA 58.483 33.333 16.68 0.00 0.00 2.43
101 102 8.327941 TGCATGCCAACTAGAATATTCTAATC 57.672 34.615 22.42 11.99 39.15 1.75
102 103 7.391554 TGCATGCCAACTAGAATATTCTAATCC 59.608 37.037 22.42 11.76 39.15 3.01
103 104 7.148171 GCATGCCAACTAGAATATTCTAATCCC 60.148 40.741 22.42 12.30 39.15 3.85
105 106 7.453393 TGCCAACTAGAATATTCTAATCCCAG 58.547 38.462 22.42 15.28 39.15 4.45
106 107 7.292356 TGCCAACTAGAATATTCTAATCCCAGA 59.708 37.037 22.42 3.85 39.15 3.86
1050 1060 1.270305 TGTGCTCACTTTCTTCCCTCG 60.270 52.381 1.47 0.00 0.00 4.63
1104 1114 1.614824 CTGCCACCTTCCTCCTCCT 60.615 63.158 0.00 0.00 0.00 3.69
1226 1308 0.613260 ATGCTACTGCCACCTTCGAA 59.387 50.000 0.00 0.00 38.71 3.71
1238 1321 1.299648 CTTCGAATCTGCCCCCACA 59.700 57.895 0.00 0.00 0.00 4.17
1404 1492 3.132925 CCAACTTTTGGCATCAAACCAG 58.867 45.455 0.00 0.00 45.17 4.00
1464 1552 2.037772 CAGCCTGGTTGTGAGTAGTTCT 59.962 50.000 1.90 0.00 0.00 3.01
1595 1684 1.682854 CATTGTTGTGTTCTGCCCACT 59.317 47.619 0.00 0.00 33.92 4.00
1669 1758 2.950781 TCCTCGGTCTGCTTCTGATAT 58.049 47.619 0.00 0.00 0.00 1.63
1855 1944 7.703058 TTTCTCCAAGGTAATGAGGATTTTC 57.297 36.000 0.00 0.00 0.00 2.29
2151 2249 4.520874 AGCTTTTTCTTTTCTCTGGTAGGC 59.479 41.667 0.00 0.00 0.00 3.93
2294 2392 3.973206 TTTCATCAAAGCGGTCCTCTA 57.027 42.857 0.00 0.00 0.00 2.43
2694 2906 9.765795 CATACTATCTTTTTATTTCTCCGAGGT 57.234 33.333 0.00 0.00 0.00 3.85
2725 2937 5.252547 TCTTGCATTTTGTATGTGGAGCTA 58.747 37.500 0.00 0.00 0.00 3.32
2735 2947 5.512298 TGTATGTGGAGCTAACACCTAGTA 58.488 41.667 15.97 0.74 38.05 1.82
2968 3180 2.526304 TACATGTATCGAGCTTGGGC 57.474 50.000 0.08 0.00 39.06 5.36
2993 3205 0.842030 ATCTTGGACTGGAGCACCCA 60.842 55.000 0.00 0.00 44.25 4.51
3037 3249 4.530946 ACATAGTGCTAACCAGGTACTTGT 59.469 41.667 4.10 0.00 34.60 3.16
3137 3349 1.097232 CGCCATTCATTTGAGAGGCA 58.903 50.000 19.05 0.00 42.34 4.75
3156 3368 8.079211 AGAGGCATGTAAAGATCTACAACTAA 57.921 34.615 2.50 0.00 35.48 2.24
3280 3493 3.679389 CAGGACTGGTTGCTCAAGTTAT 58.321 45.455 0.00 0.00 0.00 1.89
3344 3557 7.667219 CCCTGGATATATAAAGTTTGTGCAGAT 59.333 37.037 0.00 0.00 0.00 2.90
3486 3699 7.581011 AACAAAGTTCATGTTGTCAGAAAAC 57.419 32.000 0.00 0.00 39.43 2.43
3531 3745 5.045668 TGATGATTGTTGTGTGTATGCAC 57.954 39.130 7.03 7.03 45.44 4.57
3664 3882 4.243793 TGAAGGGTGTTTTCCTTGAGAA 57.756 40.909 0.00 0.00 43.98 2.87
3870 4409 1.142748 AGCTCGCGAGATCAAAGGG 59.857 57.895 38.74 11.21 40.84 3.95
3935 4474 6.255237 CGAAGATATGCATTAGAGATTGCGAT 59.745 38.462 3.54 0.00 41.80 4.58
4008 4548 5.342866 ACCTCTTCAGTTTGGGACTATAGT 58.657 41.667 4.68 4.68 36.65 2.12
4344 4889 8.551205 GGAATTTTTCCTTTTCAAATGTCAGAC 58.449 33.333 0.00 0.00 46.57 3.51
4425 4971 9.898152 AAATCCTGAGGTTCAAATTTTTAAACA 57.102 25.926 0.00 0.00 0.00 2.83
4426 4972 9.546428 AATCCTGAGGTTCAAATTTTTAAACAG 57.454 29.630 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.578576 TTTAACATGATACGGTATCTACCTACT 57.421 33.333 24.27 8.86 44.25 2.57
13 14 7.817962 GCATTTAACATGATACGGTATCTACCT 59.182 37.037 24.27 12.01 44.25 3.08
14 15 7.201410 CGCATTTAACATGATACGGTATCTACC 60.201 40.741 24.27 4.08 42.98 3.18
15 16 7.539710 TCGCATTTAACATGATACGGTATCTAC 59.460 37.037 24.27 4.40 36.17 2.59
16 17 7.595604 TCGCATTTAACATGATACGGTATCTA 58.404 34.615 24.27 13.77 36.17 1.98
17 18 6.452242 TCGCATTTAACATGATACGGTATCT 58.548 36.000 24.27 10.32 36.17 1.98
18 19 6.699895 TCGCATTTAACATGATACGGTATC 57.300 37.500 18.97 18.97 35.74 2.24
19 20 6.402118 GCATCGCATTTAACATGATACGGTAT 60.402 38.462 0.00 0.00 0.00 2.73
20 21 5.107259 GCATCGCATTTAACATGATACGGTA 60.107 40.000 0.00 0.00 0.00 4.02
21 22 4.319477 GCATCGCATTTAACATGATACGGT 60.319 41.667 0.00 0.00 0.00 4.83
22 23 4.151070 GCATCGCATTTAACATGATACGG 58.849 43.478 0.00 0.00 0.00 4.02
23 24 4.151070 GGCATCGCATTTAACATGATACG 58.849 43.478 0.00 0.00 0.00 3.06
24 25 5.107109 TGGCATCGCATTTAACATGATAC 57.893 39.130 0.00 0.00 0.00 2.24
25 26 5.764487 TTGGCATCGCATTTAACATGATA 57.236 34.783 0.00 0.00 0.00 2.15
26 27 4.652421 TTGGCATCGCATTTAACATGAT 57.348 36.364 0.00 0.00 0.00 2.45
27 28 4.652421 ATTGGCATCGCATTTAACATGA 57.348 36.364 0.00 0.00 0.00 3.07
28 29 5.063691 ACAAATTGGCATCGCATTTAACATG 59.936 36.000 0.00 0.00 0.00 3.21
29 30 5.063691 CACAAATTGGCATCGCATTTAACAT 59.936 36.000 0.00 0.00 0.00 2.71
30 31 4.388165 CACAAATTGGCATCGCATTTAACA 59.612 37.500 0.00 0.00 0.00 2.41
31 32 4.388469 ACACAAATTGGCATCGCATTTAAC 59.612 37.500 0.00 0.00 0.00 2.01
32 33 4.564041 ACACAAATTGGCATCGCATTTAA 58.436 34.783 0.00 0.00 0.00 1.52
33 34 4.172505 GACACAAATTGGCATCGCATTTA 58.827 39.130 0.00 0.00 30.77 1.40
34 35 2.995258 GACACAAATTGGCATCGCATTT 59.005 40.909 0.00 0.00 30.77 2.32
35 36 2.029200 TGACACAAATTGGCATCGCATT 60.029 40.909 0.00 0.00 38.87 3.56
36 37 1.545136 TGACACAAATTGGCATCGCAT 59.455 42.857 0.00 0.00 38.87 4.73
37 38 0.957362 TGACACAAATTGGCATCGCA 59.043 45.000 0.00 0.00 38.87 5.10
38 39 3.790744 TGACACAAATTGGCATCGC 57.209 47.368 0.00 0.00 38.87 4.58
43 44 2.004017 CCATGCATGACACAAATTGGC 58.996 47.619 28.31 0.00 0.00 4.52
44 45 2.004017 GCCATGCATGACACAAATTGG 58.996 47.619 28.31 9.81 0.00 3.16
45 46 2.689646 TGCCATGCATGACACAAATTG 58.310 42.857 28.31 8.75 31.71 2.32
46 47 3.404224 TTGCCATGCATGACACAAATT 57.596 38.095 28.31 0.00 38.76 1.82
47 48 3.620427 ATTGCCATGCATGACACAAAT 57.380 38.095 28.31 10.43 38.76 2.32
48 49 4.532314 TTATTGCCATGCATGACACAAA 57.468 36.364 28.31 15.45 38.76 2.83
49 50 4.532314 TTTATTGCCATGCATGACACAA 57.468 36.364 28.31 25.14 38.76 3.33
50 51 4.739587 ATTTATTGCCATGCATGACACA 57.260 36.364 28.31 18.81 38.76 3.72
51 52 6.448852 TCATATTTATTGCCATGCATGACAC 58.551 36.000 28.31 16.49 38.76 3.67
52 53 6.651975 TCATATTTATTGCCATGCATGACA 57.348 33.333 28.31 20.53 38.76 3.58
53 54 6.035650 GCATCATATTTATTGCCATGCATGAC 59.964 38.462 28.31 17.77 38.76 3.06
54 55 6.103330 GCATCATATTTATTGCCATGCATGA 58.897 36.000 28.31 8.76 38.76 3.07
55 56 5.872070 TGCATCATATTTATTGCCATGCATG 59.128 36.000 20.19 20.19 40.06 4.06
56 57 6.043854 TGCATCATATTTATTGCCATGCAT 57.956 33.333 0.00 0.00 40.06 3.96
57 58 5.470047 TGCATCATATTTATTGCCATGCA 57.530 34.783 0.00 0.00 42.09 3.96
58 59 5.220586 GCATGCATCATATTTATTGCCATGC 60.221 40.000 14.21 0.00 39.69 4.06
59 60 5.293324 GGCATGCATCATATTTATTGCCATG 59.707 40.000 21.36 0.00 38.46 3.66
60 61 5.046231 TGGCATGCATCATATTTATTGCCAT 60.046 36.000 21.36 0.00 42.77 4.40
61 62 4.283722 TGGCATGCATCATATTTATTGCCA 59.716 37.500 21.36 17.02 44.99 4.92
62 63 4.823157 TGGCATGCATCATATTTATTGCC 58.177 39.130 21.36 12.56 38.99 4.52
63 64 5.929992 AGTTGGCATGCATCATATTTATTGC 59.070 36.000 21.36 0.00 35.67 3.56
64 65 8.517056 TCTAGTTGGCATGCATCATATTTATTG 58.483 33.333 21.36 0.00 0.00 1.90
65 66 8.640063 TCTAGTTGGCATGCATCATATTTATT 57.360 30.769 21.36 0.00 0.00 1.40
66 67 8.640063 TTCTAGTTGGCATGCATCATATTTAT 57.360 30.769 21.36 0.00 0.00 1.40
67 68 8.640063 ATTCTAGTTGGCATGCATCATATTTA 57.360 30.769 21.36 0.00 0.00 1.40
68 69 6.964807 TTCTAGTTGGCATGCATCATATTT 57.035 33.333 21.36 0.00 0.00 1.40
69 70 8.818622 ATATTCTAGTTGGCATGCATCATATT 57.181 30.769 21.36 0.32 0.00 1.28
70 71 8.818622 AATATTCTAGTTGGCATGCATCATAT 57.181 30.769 21.36 6.32 0.00 1.78
71 72 8.105197 AGAATATTCTAGTTGGCATGCATCATA 58.895 33.333 21.36 5.92 35.34 2.15
72 73 6.946583 AGAATATTCTAGTTGGCATGCATCAT 59.053 34.615 21.36 4.96 35.34 2.45
73 74 6.301486 AGAATATTCTAGTTGGCATGCATCA 58.699 36.000 21.36 6.25 35.34 3.07
74 75 6.814506 AGAATATTCTAGTTGGCATGCATC 57.185 37.500 21.36 8.90 35.34 3.91
75 76 8.874744 ATTAGAATATTCTAGTTGGCATGCAT 57.125 30.769 21.36 8.62 40.57 3.96
76 77 7.391554 GGATTAGAATATTCTAGTTGGCATGCA 59.608 37.037 21.36 2.54 40.57 3.96
77 78 7.148171 GGGATTAGAATATTCTAGTTGGCATGC 60.148 40.741 21.40 9.90 40.57 4.06
78 79 7.884877 TGGGATTAGAATATTCTAGTTGGCATG 59.115 37.037 21.40 0.00 40.57 4.06
79 80 7.988937 TGGGATTAGAATATTCTAGTTGGCAT 58.011 34.615 21.40 13.13 40.57 4.40
80 81 7.292356 TCTGGGATTAGAATATTCTAGTTGGCA 59.708 37.037 21.40 9.38 40.57 4.92
81 82 7.680730 TCTGGGATTAGAATATTCTAGTTGGC 58.319 38.462 21.40 9.88 40.57 4.52
111 112 7.363793 GGTTGGCTGTGATCCAAATAGTTATTT 60.364 37.037 0.00 0.00 44.36 1.40
842 849 3.818787 GGGCGTCGTCGGAAGCTA 61.819 66.667 3.90 0.00 45.45 3.32
888 895 1.459455 CGAGGAGGATGGATGCGTCT 61.459 60.000 5.77 0.00 0.00 4.18
1129 1151 2.811317 CGCAGCGACTCTGTTCCC 60.811 66.667 9.98 0.00 44.66 3.97
1255 1338 1.134551 GTAGAAGAGAGGGCAGCTTGG 60.135 57.143 0.00 0.00 0.00 3.61
1257 1340 2.246091 AGTAGAAGAGAGGGCAGCTT 57.754 50.000 0.00 0.00 0.00 3.74
1404 1492 6.254281 ACAGAACACAACCAATAGCATAAC 57.746 37.500 0.00 0.00 0.00 1.89
1464 1552 2.948979 AGTTCGTCCAACTGCATTTGAA 59.051 40.909 17.60 0.00 44.28 2.69
1653 1742 6.091849 CCAAATATGATATCAGAAGCAGACCG 59.908 42.308 11.78 0.00 0.00 4.79
1669 1758 8.988060 TGTGGTTAACTAGAGATCCAAATATGA 58.012 33.333 5.42 0.00 0.00 2.15
1855 1944 1.766494 TATGCTGCAGAAACCATGGG 58.234 50.000 20.43 0.00 0.00 4.00
2007 2105 6.094603 ACTCAGATATTTGATGTTTGACTGGC 59.905 38.462 0.00 0.00 0.00 4.85
2047 2145 0.252103 AAGCCCCGAGTGAGACCTTA 60.252 55.000 0.00 0.00 0.00 2.69
2141 2239 2.930682 GCTAACGAAAAGCCTACCAGAG 59.069 50.000 0.00 0.00 33.73 3.35
2151 2249 3.220350 CGATAAGCCGCTAACGAAAAG 57.780 47.619 0.00 0.00 43.93 2.27
2505 2633 1.227823 CACAGGGAGTTGTCGCCAA 60.228 57.895 0.00 0.00 36.26 4.52
2526 2654 5.163269 TGCAGATAAGCAACTCATGTCCTAT 60.163 40.000 0.00 0.00 42.46 2.57
2694 2906 7.598118 CCACATACAAAATGCAAGATAAACACA 59.402 33.333 0.00 0.00 0.00 3.72
2725 2937 8.522542 TTTAACCAATGTTTGTACTAGGTGTT 57.477 30.769 0.00 0.00 35.87 3.32
2735 2947 9.308318 GACAAGTACATTTTAACCAATGTTTGT 57.692 29.630 16.08 16.08 43.54 2.83
2801 3013 3.290948 GGCAACCAAGGGATATGTACA 57.709 47.619 0.00 0.00 0.00 2.90
2949 3161 1.269569 CGCCCAAGCTCGATACATGTA 60.270 52.381 8.27 8.27 36.60 2.29
2958 3170 2.202932 ATACTGCGCCCAAGCTCG 60.203 61.111 4.18 0.00 38.13 5.03
2968 3180 1.804372 GCTCCAGTCCAAGATACTGCG 60.804 57.143 0.00 0.00 42.47 5.18
2993 3205 0.886490 CCTTTCTTGGCGCTGTGTCT 60.886 55.000 7.64 0.00 0.00 3.41
3069 3281 4.321899 GCAAAATTCCAGACAACATGCCTA 60.322 41.667 0.00 0.00 0.00 3.93
3156 3368 0.468226 TCCCGCTTCTCACAACTGTT 59.532 50.000 0.00 0.00 0.00 3.16
3280 3493 1.476891 CTAGCTTACAGGCTCCGTCAA 59.523 52.381 0.00 0.00 42.97 3.18
3315 3528 6.040391 GCACAAACTTTATATATCCAGGGCAA 59.960 38.462 0.00 0.00 0.00 4.52
3344 3557 2.355310 GGTGATGGTTCGTTGGGTCATA 60.355 50.000 0.00 0.00 0.00 2.15
3935 4474 3.053991 AGAGCCAGACTAGTGAGAGCTTA 60.054 47.826 0.00 0.00 0.00 3.09
4008 4548 6.310956 TCGTAGTCGTGACTTTTCAAAAGAAA 59.689 34.615 17.05 1.23 42.54 2.52
4109 4649 6.717540 ACAATATGCCACAAGTACCAAAGTTA 59.282 34.615 0.00 0.00 0.00 2.24
4425 4971 0.940126 CTTGCGTGCACTTGTTCTCT 59.060 50.000 16.19 0.00 0.00 3.10
4426 4972 0.657840 ACTTGCGTGCACTTGTTCTC 59.342 50.000 16.19 0.00 0.00 2.87


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.